257 Matching Annotations
  1. Aug 2022
    1. noise can alternatively be defined as theinformation lost between input and output. We term this as ‘noise in input’ at the regulator end,20and ‘noise in output’ at the effector end

      Different definition of noise here!

    2. In some cases, greater variance facilitates better regulation

      Sometimes noise good

    3. A higher Shannon entropy indicates that the probabilitydistribution of gene expression becomes more uniform, thereby decreasing the ability to reliablypredict gene expression.

      high shannon entropy = less signal, needs more clarification to understand what's going on. low entropy = more signal, can more easily understand what's going on

    4. Collectively, these data suggest that aging may be accompanied by areallocation of resources that favor messages crucial to maintenance of stability and survival.

      wow wow wow!

    1. Free radicals,ionizingradiation,

      literature has deviated from these as causes of aging

    2. Although the model is concise(an organism is considered as a simple set of cells)

      this is a flaw. need to account for ECM and other things outside of domain of cells

    Annotators

  2. Jul 2022
    1. pleiotropic

      having multiple phenotypic expressions a pleiotropic gene.

    Annotators

  3. Jun 2022
    1. BSA
    2. 10xChromium to capture single cell transcriptomes.
    3. samplemultiplexing (
    4. PBS
    5. perfused

      permeated with

    6. FACS

      FACS = flow cytometry, used to analyze chemical property of cells

    7. We then generated 79,488 single cell transcriptomes from the SVZ neurogenic regionfrom young (5 month) and old (23 month),

      why so many more transcriptomes?

    8. However, shared genes carry a disproportionate weight within theclocks, with coefficients approximately 40% larger in magnitude

      do they "contribute" more to aging? is that what they're trying to say

    9. (R = 0.41-0.89, error = 2.3 - 4.6 months)

      more precise, less accurate than chronological aging clock they made

    10. Even though all clocks were trained on aNSC-NPC‘proliferative fraction’, the microglia and oligodendrocytes biological age clocks performedbetter than aNSC-NPC ones.

      so the biological aging clock performed better on non trained cell types than the cell types it train on?

    1. MTR

      missing tissue response

    2. One hypothesis is that general prolif-eration can combine with positional informationto up-regulate any regionally specified progenitorclass neara wound, regardless of whether its targettissue is missing

      To paraphrase, if a region of the planarian is wounded, local tissue specific neoblasts to that region will proliferate whether or not the tissue they compose is the one that is damaged

    3. issue-specific resection of planarianeyes does not cause up-regulation of eye progen-itors. In this case, eye regeneration is explainedby a constitutive basal rate of eye progenitor pro-duction and the fact that newly regenerating eyesare constituted by young cells and have fewertotal cells that could die per unit time

      there is a constant upkeep of progenitor cells for X tissue it seems. and when X tissue is damaged, newly produced progenitor cells from that regular rate of renewal come to the rescue (yet there is no upregulation of them it seems)

    4. he tgs-1 tran-script itself perdures in a subset of G1-annotatedneoblasts with neural markers;

      so is the lack of FSTF markers in pre mitotic neoblasts inconsistent. i.e. here in neural specialized neoblasts the marker is present during G1

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  4. May 2022
    1. neoblast) being FSTF transcript-low and thesmedwi-1-low daughter (a postmitotic differen-tiating cell) being FSTF-transcript high

      so when a neoblast divides, one of the daughter cells differentiates (high FSTF) while the other stays neoblast (high smedwi-1)?

    2. In this model, a specialized neoblast can divideto produce cells with asymmetric outcomes,with one daughter being a neoblast capable ofchoosing a new fate in its next round of celldivision

      what does this mean

    3. smedwi-1
    4. Single-step fatemodel. Neoblasts can choose a fate and produce a differentiated cell in the course of a single cell division.

      so no transit amplifying cells like in humans

    5. sin-gle-cell qPCR

      used to to determine what genes are being expressed in each cell.

    6. mesenchymal

      cells that develop into connective tissue, blood vessels, and lymphatic tissue.

    7. Because a smallplanarian fragment must accomplish regenera-tion with existing mass, blastemas cannotregrow all missing tissues at their original scale

      like that deadpool scene? lol

    Annotators

  5. Mar 2022
    1. to initiate exit from pluripotency and to restrict cells to spe-cific differentiation paths.

      aka how to not get cancer

    2. opens thequestion as to how regeneration signals instruct PSCs to pro-duce the appropriate number and type of progenitor neoblastsin response to different regeneration requirements.

      boy do i have a scientist for you...

    3. soxP-3

      is this similar to https://en.wikipedia.org/wiki/SOX2 ?

    4. Therefore, high levels of PIWI-1 protein appear pri-marily associated with actively dividing cells,

      maybe why it's associated with cancer

    5. a heterogeneous number of piwi-1 transcripts

      varying cell to cell

    6. clonal expansion

      The clonal selection theory, as we know it today, posits that cells naturally and stochastically express antigen receptors (that is, without the influence of antigen), and that antigen drives the proliferation and differentiation of cells with specific antigen receptors.

    7. Only 7 out of120 injected neoblasts resulted in successful restoration of hostviability, suggesting extensive functional heterogeneity in theneoblast population

      was this an issue with the neoblast or the mouse

    8. ingle-cell transplantations demon-strated that a single neoblast is capable of rescuing lethally irra-diated hosts by reconstituting all cell types in the animal’s body

      so this one progenitor cell replicated and regenerated all of the damaged tissues in the mouse?

    Annotators

    1. indicating a highly significant association between induction of cellular stress resistance and C. elegans longevity

      Ok yay

    2. However, 16/54 negative control compounds tested (i.e., those that did not induce MTF stress resistance) were also able to significantly increase fly lifespan (29.6% of the total compounds tested; p=0.07 for hits versus negative controls)

      Rip

    3. Among the 70 unique compounds that significantly increased MTF stress resistance that were tested in flies, 12 significantly increased fly lifespan in either or both sexes (17.1% of the total compounds tested)

      Very high ratio!!!

    4. optimizing growth media, seeding density, and incubation time.

      the higher these numbers are, the better?

  6. Jan 2022
    1. 560 (

      but not after whole numbers for whatever reason

    2. 0.0200

      Everything after a number in decimal form counts

    3. 0.02

      0s before a decimal don't count

    4. 1005

      Every 0 in between whole number counts as a sig fig.

      17002 has 5 sig figs

    Annotators

    1. low dose of doxycycline

      doxycycline dose matters, too much cause cancer

    2. metabolites

      intermediate or end product of metabolism

    3. hematopoietic cells

      this is a stem cell; why would it age?

    4. As expected, all of these were increased with aging; however, their levels 273 did not decline in any of the two cohorts of very old-OSKM mice

      cellular senescence not reversed

    5. Interestingly, the large majority of genes 188 upregulated by OSKM in old mice (pink dots) corresponded to genes with 189 reduced expression upon aging

      why is this interesting?

    6. We conclude that a single period 172 of OSKM expression is able to rejuvenate a fraction of the methylation changes 173 that occur with aging in promoters and enhancers.

      would multiple cycles of partial reprogramming add on to this rejuvenation or would it be diminishing returns?

      would the same promoters be rolled back or would new ones be reprogrammed?

    7. (“very old”, n=6), 147 and reprogrammable mice

      what do they mean by "reprogrammable" mice?

    8. MspI-based Reduced Representation Bisulfite 96 Sequencing

      a very good way of detecting dna methylation

    9. the histological changes 81 observed in the pancreas after one week of OSKM induction were reversed two 82 weeks after removal of doxycycline

      one week of OSKM = partial reprogramming. two weeks OSKM = pluripotentcy (shown by expression of NANOG).

      Major changes in appearance of tissue (histology) reversed after 2 weeks

    10. dysplasia in which the tissue alters its normal architecture 66 and cells lose differentiation markers

      dysplasia = loss of identity; cell types non native to a tissue emerging

  7. Jul 2021
    1. (Or shelter hah) the end of the telomere from the DNA repair machinery: DNA looks like a continuous strand for most of its length except at the ends, so it is efficient for the cell to recognise 'ends' of this strand as breaks, and try to repair them. But of course you wouldn't want that in the end of the chromosome, because it's a legitimate feature. However, if true damage happens to the telomeric section, it's not going to be repaired, so telomeres steadily accumulate damage.

      I feel like this could be elaborated on. To my understanding, the shelterin protein on the ends of telomeres prevents telomeres from being repaired when they're actually damaged - is that what you mean?

    2. there is support for continued trials of metformin in humans, and there is some evidence that it could improve diseases associated with aging; however we still don't know if it would help with increasing maximum lifespan in humans.

      I would add that there is some evidence the earlier you take metoformin, the better its effect will be https://pubmed.ncbi.nlm.nih.gov/21386129/

    3. C. Elegant

      joke or typo?